lecture 1.2 - case 10 DNA
selection/domestication:
what changes have occurred in the genomes of these animals and what did we
learn from it?
Wild- domestication domestication- wild
Origin domestication Commercialization; process where you have extreme
traits
Breeds present due to combined factors:
1. Geographical isolation
2. Selection for desired characteristics
3. Behavioral traits
Breeds distinguished by physical traits:
1. Size, plumage color, comb type, skin color, number
of toes, amount of feathering, egg color and place of origin.
2. Primary use: eggs, meat, ornamental purposes
draft genome sequencing
Why was the chicken the first animal species with a sequenced genome?
- Model species in embryology and development
- Agricultural relevance
- Phylogenic position
- Good genomic resources
The chicken has multiple similarities (and differences) with the human genome.
- Chicken genome is 3x less genome as mammals (1,06 billion bp). Which
makes it easier to sequence the genome.
- Chicken genome: 39 chromosomes (38 autosomes, 2n, and the sex
chromosomes Z and W, in which female is ZW and male is ZZ)
- Inbred loses genetic variation. Problems within the off spring.
Used: Shotgun method: multiple gene particles, which need to be aligned.
When markers are close, the inheritance is more likely to be the same. When
markers are far away from each other, inheritance is less likely to be the same.
How?
Genomic DNA cut DNA add linkers to the pieces DNA look for overlap =
sequencing
, - Look for the variation in the sequence, which gives information about
multiple different characteristics. (more important than the sequence
itself)
- Variation: SNPs (these snips are used for selection) and CNVs (# of
variation).
What can be sequenced:
- DNA, structure of chromosomes
- RNA, gene expression (active and unactive, mutation effect and for which
reasons)
Proteome
A proteome is the entire set of proteins that’s expressed by a genome, cell,
tissue.
Regulatory proteins have influence on gene expression (because regulate
proteins made, so regulate phenotype):
- Enhancers
- Suppressors
- Silencer
- Insulator
Which when mutated, may have a changed original influence on gene expression,
cause proteins made is affected.
A substitution in the promotor of a gene may change the regulation in the
quantity of protein with which a gene is expressed. If a substitution occurs in an
intron, often nothing will change, but it may also be that the SNP is
60% of the chicken genes show a 1:1 orthologous relationship with human genes.
- Homologous: genes with the same function but a difference in location.
Chicken – human orthologs exhibit on average 75% amino acid identity.
conserved synteny
Synteny: A situation in which genes are arranged in similar blocks in different
species.
- Comparative genomics to find functional sequences
Regulatory elements
Direct alignments: conservation jungles and gene deserts
- Gene deserts: long regions in the genome without genes.
- In humans the largest gene deserts is on chromosome 19, which is 5,1 Mb,
and also the chromosome with the most gene dense.
- 545 human regions > 640 kb, regular intergenic region: 6 – 72 kb
Conserved clusters of TFBS
selection/domestication:
what changes have occurred in the genomes of these animals and what did we
learn from it?
Wild- domestication domestication- wild
Origin domestication Commercialization; process where you have extreme
traits
Breeds present due to combined factors:
1. Geographical isolation
2. Selection for desired characteristics
3. Behavioral traits
Breeds distinguished by physical traits:
1. Size, plumage color, comb type, skin color, number
of toes, amount of feathering, egg color and place of origin.
2. Primary use: eggs, meat, ornamental purposes
draft genome sequencing
Why was the chicken the first animal species with a sequenced genome?
- Model species in embryology and development
- Agricultural relevance
- Phylogenic position
- Good genomic resources
The chicken has multiple similarities (and differences) with the human genome.
- Chicken genome is 3x less genome as mammals (1,06 billion bp). Which
makes it easier to sequence the genome.
- Chicken genome: 39 chromosomes (38 autosomes, 2n, and the sex
chromosomes Z and W, in which female is ZW and male is ZZ)
- Inbred loses genetic variation. Problems within the off spring.
Used: Shotgun method: multiple gene particles, which need to be aligned.
When markers are close, the inheritance is more likely to be the same. When
markers are far away from each other, inheritance is less likely to be the same.
How?
Genomic DNA cut DNA add linkers to the pieces DNA look for overlap =
sequencing
, - Look for the variation in the sequence, which gives information about
multiple different characteristics. (more important than the sequence
itself)
- Variation: SNPs (these snips are used for selection) and CNVs (# of
variation).
What can be sequenced:
- DNA, structure of chromosomes
- RNA, gene expression (active and unactive, mutation effect and for which
reasons)
Proteome
A proteome is the entire set of proteins that’s expressed by a genome, cell,
tissue.
Regulatory proteins have influence on gene expression (because regulate
proteins made, so regulate phenotype):
- Enhancers
- Suppressors
- Silencer
- Insulator
Which when mutated, may have a changed original influence on gene expression,
cause proteins made is affected.
A substitution in the promotor of a gene may change the regulation in the
quantity of protein with which a gene is expressed. If a substitution occurs in an
intron, often nothing will change, but it may also be that the SNP is
60% of the chicken genes show a 1:1 orthologous relationship with human genes.
- Homologous: genes with the same function but a difference in location.
Chicken – human orthologs exhibit on average 75% amino acid identity.
conserved synteny
Synteny: A situation in which genes are arranged in similar blocks in different
species.
- Comparative genomics to find functional sequences
Regulatory elements
Direct alignments: conservation jungles and gene deserts
- Gene deserts: long regions in the genome without genes.
- In humans the largest gene deserts is on chromosome 19, which is 5,1 Mb,
and also the chromosome with the most gene dense.
- 545 human regions > 640 kb, regular intergenic region: 6 – 72 kb
Conserved clusters of TFBS
